getFeaturesInClusterList: Get feature names in selected cluster

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Get feature names in selected cluster

Description

Get feature names in selected cluster given array of chrom and cluster ids

Usage

getFeaturesInClusterList(treeListClusters, chrom, clustID, id)

Arguments

treeListClusters	from createClusters()
chrom	chromosome name of cluster
clustID	cluster identifier
id	clustering parameter identifier

Value

list of array of feature names. Query with index i as returned in list index i

Examples

library(GenomicRanges)

data('decorateData')

# Evaluate hierarchical clustering
treeList = runOrderedClusteringGenome( simData, simLocation ) 

# Choose cutoffs and return clusters
treeListClusters = createClusters( treeList, method='meanClusterSize', meanClusterSize = 50 )

df_cluster = data.frame( chrom = c("chr20", "chr20"), 
  cluster = c(3,5), 
  id = c("50", "50"), stringsAsFactors=FALSE )

# Find features for the clusters in df_cluster
getFeaturesInClusterList( treeListClusters, chrom=df_cluster$chrom, clustID=df_cluster$cluster, id=df_cluster$id)

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.